COX7A1

cytochrome c oxidase subunit 7A1, the group of Mitochondrial complex IV: cytochrome c oxidase subunits

Basic information

Region (hg38): 19:36150922-36152449

Previous symbols: [ "COX7A" ]

Links

ENSG00000161281

∙ NCBI:1346 ∙ OMIM:123995 ∙ HGNC:2287 ∙ Uniprot:P24310 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COX7A1 gene.

not_specified (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX7A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001864.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX7A1	protein_coding	protein_coding	ENST00000292907	4	1948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000373	0.223	125700	0	9	125709	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.549	39	49.9	0.781	0.00000330	496
Missense in Polyphen		14	19.383	0.72228		210
Synonymous	1.11	14	20.4	0.688	0.00000125	149
Loss of Function	-0.532	6	4.75	1.26	2.55e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000967	0.0000967
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000311	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.;
Pathway: Cardiac muscle contraction - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Electron Transport Chain (Consensus)

Recessive Scores

pRec: 0.127

Intolerance Scores

loftool: 0.756
rvis_EVS: -0.01
rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

pHI: 0.125
hipred: N
hipred_score: 0.213
ghis: 0.481

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0628

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Cox7a1
Phenotype: cellular phenotype; muscle phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype;

Gene ontology

Biological process: regulation of oxidative phosphorylation;generation of precursor metabolites and energy;electron transport chain;mitochondrial respirasome assembly;proton transmembrane transport
Cellular component: mitochondrion;mitochondrial respirasome;integral component of membrane
Molecular function: cytochrome-c oxidase activity